当前位置： SCI文献检索 > PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA期刊下所有文献 > Reverse engineering dynamic temporal models of biological processes and their relationships.

Reverse engineering dynamic temporal models of biological processes and their relationships.

Abstract：

:Biological processes such as circadian rhythms, cell division, metabolism, and development occur as ordered sequences of events. The synchronization of these coordinated events is essential for proper cell function, and hence the determination of critical time points in biological processes is an important component of all biological investigations. In particular, such critical time points establish logical ordering constraints on subprocesses, impose prerequisites on temporal regulation and spatial compartmentalization, and situate dynamic reorganization of functional elements in preparation for subsequent stages. Thus, building temporal phenomenological representations of biological processes from genome-wide datasets is relevant in formulating biological hypotheses on: how processes are mechanistically regulated; how the regulations vary on an evolutionary scale, and how their inadvertent disregulation leads to a diseased state or fatality. This paper presents a general framework (GOALIE) to reconstruct temporal models of cellular processes from time-course gene expression data. We mathematically formulate the problem as one of optimally segmenting datasets into a succession of "informative" windows such that time points within a window expose concerted clusters of gene action whereas time points straddling window boundaries constitute points of significant restructuring. We illustrate here how GOALIE successfully brings out the interplay between multiple yeast processes, inferred from combined experimental datasets for the cell cycle and the metabolic cycle.

journal_name

Proc Natl Acad Sci U S A

journal_title

Proceedings of the National Academy of Sciences of the United States of America

authors

Ramakrishnan N,Tadepalli S,Watson LT,Helm RF,Antoniotti M,Mishra B

doi

10.1073/pnas.1006283107

subject

Has Abstract

pub_date

2010-07-13 00:00:00

pages

12511-6

issue

28

eissn

0027-8424

issn

1091-6490

pii

1006283107

journal_volume

107

pub_type

杂志文章

相关文献

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA文献大全
  • Capping protein regulates actin dynamics during cytokinetic midbody maturation.

    abstract：:During cytokinesis, a cleavage furrow generated by actomyosin ring contraction is restructured into the midbody, a platform for the assembly of the abscission machinery that controls the final separation of daughter cells. The polymerization state of F-actin is important during assembly, ingression, disassembly, and c...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1722281115

    authors： Terry SJ,Donà F,Osenberg P,Carlton JG,Eggert US

    更新日期：2018-02-27 00:00:00

  • Optimal decision making and matching are tied through diminishing returns.

    abstract：:How individuals make decisions has been a matter of long-standing debate among economists and researchers in the life sciences. In economics, subjects are viewed as optimal decision makers who maximize their overall reward income. This framework has been widely influential, but requires a complete knowledge of the rew...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1703440114

    authors： Kubanek J

    更新日期：2017-08-08 00:00:00

  • Splicing inhibition of U2AF65 leads to alternative exon skipping.

    abstract：:U2 snRNP auxiliary factor 65 kDa (U2AF(65)) is a general splicing factor that contacts polypyrimidine (Py) tract and promotes prespliceosome assembly. In this report, we show that U2AF(65) stimulates alternative exon skipping in spinal muscular atrophy (SMA)-related survival motor neuron (SMN) pre-mRNA. A stronger 5' ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1500639112

    authors： Cho S,Moon H,Loh TJ,Jang HN,Liu Y,Zhou J,Ohn T,Zheng X,Shen H

    更新日期：2015-08-11 00:00:00

  • Retinal prosthetic strategy with the capacity to restore normal vision.

    abstract：:Retinal prosthetics offer hope for patients with retinal degenerative diseases. There are 20-25 million people worldwide who are blind or facing blindness due to these diseases, and they have few treatment options. Drug therapies are able to help a small fraction of the population, but for the vast majority, their bes...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1207035109

    authors： Nirenberg S,Pandarinath C

    更新日期：2012-09-11 00:00:00

  • Metabolic connectivity mapping reveals effective connectivity in the resting human brain.

    abstract：:Directionality of signaling among brain regions provides essential information about human cognition and disease states. Assessing such effective connectivity (EC) across brain states using functional magnetic resonance imaging (fMRI) alone has proven difficult, however. We propose a novel measure of EC, termed metabo...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1513752113

    authors： Riedl V,Utz L,Castrillón G,Grimmer T,Rauschecker JP,Ploner M,Friston KJ,Drzezga A,Sorg C

    更新日期：2016-01-12 00:00:00

  • Evolution of chloroplast retrograde signaling facilitates green plant adaptation to land.

    abstract：:Chloroplast retrograde signaling networks are vital for chloroplast biogenesis, operation, and signaling, including excess light and drought stress signaling. To date, retrograde signaling has been considered in the context of land plant adaptation, but not regarding the origin and evolution of signaling cascades link...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1812092116

    authors： Zhao C,Wang Y,Chan KX,Marchant DB,Franks PJ,Randall D,Tee EE,Chen G,Ramesh S,Phua SY,Zhang B,Hills A,Dai F,Xue D,Gilliham M,Tyerman S,Nevo E,Wu F,Zhang G,Wong GK,Leebens-Mack JH,Melkonian M,Blatt MR,Soltis P

    更新日期：2019-03-12 00:00:00

  • A gene required for transfer of T-DNA to plants encodes an ATPase with autophosphorylating activity.

    abstract：:The virB operon of the Agrobacterium tume-faciens pTiA6NC plasmid likely plays a role in directing T-DNA transfer events at the bacterial membrane, as determined previously by mutagenesis and cellular fractionation studies and by DNA sequence analysis of the approximately 12-kilobase-pair operon. The DNA sequence anal...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.86.24.9677

    authors： Christie PJ,Ward JE Jr,Gordon MP,Nester EW

    更新日期：1989-12-01 00:00:00

  • Acc homoeoloci and the evolution of wheat genomes.

    abstract：:The DNA sequences of wheat Acc-1 and Acc-2 loci, encoding the plastid and cytosolic forms of the enzyme acetyl-CoA carboxylase, were analyzed with a view to understanding the evolution of these genes and the origin of the three genomes in modern hexaploid wheat. Acc-1 and Acc-2 loci from each of the wheats Triticum ur...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0803981105

    authors： Chalupska D,Lee HY,Faris JD,Evrard A,Chalhoub B,Haselkorn R,Gornicki P

    更新日期：2008-07-15 00:00:00

  • Long-range structural defects by pathogenic mutations in most severe glucose-6-phosphate dehydrogenase deficiency.

    abstract：:Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common blood disorder, presenting multiple symptoms, including hemolytic anemia. It affects 400 million people worldwide, with more than 160 single mutations reported in G6PD. The most severe mutations (about 70) are classified as class I, leading to more...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.2022790118

    authors： Horikoshi N,Hwang S,Gati C,Matsui T,Castillo-Orellana C,Raub AG,Garcia AA,Jabbarpour F,Batyuk A,Broweleit J,Xiang X,Chiang A,Broweleit R,Vöhringer-Martinez E,Mochly-Rosen D,Wakatsuki S

    更新日期：2021-01-26 00:00:00

  • Hypothalamic extended synaptotagmin-3 contributes to the development of dietary obesity and related metabolic disorders.

    abstract：:The C2 domain containing protein extended synaptotagmin (E-Syt) plays important roles in both lipid homeostasis and the intracellular signaling; however, its role in physiology remains largely unknown. Here, we show that hypothalamic E-Syt3 plays a critical role in diet-induced obesity (DIO). E-Syt3 is characteristica...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.2004392117

    authors： Zhang Y,Guan Y,Pan S,Yan L,Wang P,Chen Z,Shen Q,Zhao F,Zhang X,Li J,Li J,Cai D,Zhang G

    更新日期：2020-08-18 00:00:00

  • Amino acid substitutions in the floor of the putative antigen-binding site of H-2T22 affect recognition by a gamma delta T-cell receptor.

    abstract：:We have previously identified a self-reactive gamma delta T-cell clone (KN6) specific for the H-2T region gene product T22b. Now we have investigated by an in vitro mutagenesis analysis of the T22b gene the possibility that the interaction between the KN6 gamma delta T-cell receptor and T22b involves a peptide. The re...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.90.23.11396

    authors： Moriwaki S,Korn BS,Ichikawa Y,van Kaer L,Tonegawa S

    更新日期：1993-12-01 00:00:00

  • Evidence for habitual climbing in a Pleistocene hominin in South Africa.

    abstract：:Bipedalism is a defining trait of the hominin lineage, associated with a transition from a more arboreal to a more terrestrial environment. While there is debate about when modern human-like bipedalism first appeared in hominins, all known South African hominins show morphological adaptations to bipedalism, suggesting...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 历史文章,杂志文章

    doi：10.1073/pnas.1914481117

    authors： Georgiou L,Dunmore CJ,Bardo A,Buck LT,Hublin JJ,Pahr DH,Stratford D,Synek A,Kivell TL,Skinner MM

    更新日期：2020-04-14 00:00:00

  • Ionizing radiation and tritium transmutation both cause formation of 5-hydroxymethyl-2'-deoxyuridine in cellular DNA.

    abstract：:HeLa cells grown in the presence of [methyl-3H]thymidine contained large amounts of 5-hydroxymethyl-2'-deoxyuridine (HMdU) in their DNA. When the cells were grown in [6-3H]thymidine and their DNA was labeled to the same specific activity, no HMdU was present. When such [6-3H]thymidine-labeled cells were exposed to inc...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.81.2.318

    authors： Teebor GW,Frenkel K,Goldstein MS

    更新日期：1984-01-01 00:00:00

  • Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations.

    abstract：:We present a simple molecular indexing method for quantitative targeted RNA sequencing, in which mRNAs of interest are selectively captured from complex cDNA libraries and sequenced to determine their absolute concentrations. cDNA fragments are individually labeled so that each molecule can be tracked from the origina...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1323732111

    authors： Fu GK,Xu W,Wilhelmy J,Mindrinos MN,Davis RW,Xiao W,Fodor SP

    更新日期：2014-02-04 00:00:00

  • Effect of glycosylation on protein folding: a close look at thermodynamic stabilization.

    abstract：:Glycosylation is one of the most common posttranslational modifications to occur in protein biosynthesis, yet its effect on the thermodynamics and kinetics of proteins is poorly understood. A minimalist model based on the native protein topology, in which each amino acid and sugar ring was represented by a single bead...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0801340105

    authors： Shental-Bechor D,Levy Y

    更新日期：2008-06-17 00:00:00

  • Negative selection on human genes underlying inborn errors depends on disease outcome and both the mode and mechanism of inheritance.

    abstract：:Genetic variants underlying life-threatening diseases, being unlikely to be transmitted to the next generation, are gradually and selectively eliminated from the population through negative selection. We study the determinants of this evolutionary process in human genes underlying monogenic diseases by comparing vario...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.2001248118

    authors： Rapaport F,Boisson B,Gregor A,Béziat V,Boisson-Dupuis S,Bustamante J,Jouanguy E,Puel A,Rosain J,Zhang Q,Zhang SY,Gleeson JG,Quintana-Murci L,Casanova JL,Abel L,Patin E

    更新日期：2021-01-19 00:00:00

  • New view of lipid bilayer dynamics from 2H and 13C NMR relaxation time measurements.

    abstract：:Natural abundance 13C spin-lattice (T1) relaxation time measurements are reported for unilamellar vesicles of 1,2-dipalmitoylphosphatidylcholine (1,2-dipalmitoyl-sn-glycero-3-phosphocholine), in the liquid crystalline phase, at magnetic field strengths of 1.40, 1.87, 2.35, 4.23, 7.05, 8.45, and 11.7 tesla (resonance f...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.80.14.4325

    authors： Brown MF,Ribeiro AA,Williams GD

    更新日期：1983-07-01 00:00:00

  • Modulation by gangliosides of the lamellar-inverted micelle (hexagonal II) phase transition in mixtures containing phosphatidylethanolamine and dioleoylglycerol.

    abstract：:We studied the effect of gangliosides GD1a and GM1 on the lamellar-to-hexagonal II phase transition of mixtures of dioleoylphosphatidylethanolamine/dioleoylphosphatidyl choline, 3:1, and of transphosphatidylated phosphatidylethanolamine with dioleoylglycerol by high-sensitivity differential scanning calorimetry, 31P-N...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.91.21.10019

    authors： Perillo MA,Scarsdale NJ,Yu RK,Maggio B

    更新日期：1994-10-11 00:00:00

  • Direct effects of 17 beta-estradiol on trabecular bone in ovariectomized rats.

    abstract：:High-affinity nuclear binding sites for 17 beta-estradiol (17 beta E2) were recently found in bone cells; however, the mechanism by which estrogen exerts its effect on bone in vivo is still unknown. To study if estrogen acts on bone directly, we used an experimental model in which test substances are infused locally i...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.87.6.2172

    authors： Takano-Yamamoto T,Rodan GA

    更新日期：1990-03-01 00:00:00

  • Different mutation signatures in DNA polymerase eta- and MSH6-deficient mice suggest separate roles in antibody diversification.

    abstract：:Hypermutation in immunoglobulin genes produces a high frequency of substitutions of all four bases, which are likely generated by low-fidelity DNA polymerases. Indeed, humans deficient for DNA polymerase (pol) eta have decreased substitutions of A.T base pairs in variable and switch regions. To study the role of pol e...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0501852102

    authors： Martomo SA,Yang WW,Wersto RP,Ohkumo T,Kondo Y,Yokoi M,Masutani C,Hanaoka F,Gearhart PJ

    更新日期：2005-06-14 00:00:00

  • DNA polymerase ζ limits chromosomal damage and promotes cell survival following aflatoxin exposure.

    abstract：:Routine dietary consumption of foods that contain aflatoxins is the second leading cause of environmental carcinogenesis worldwide. Aflatoxin-driven mutagenesis is initiated through metabolic activation of aflatoxin B1 (AFB1) to its epoxide form that reacts with N7 guanine in DNA. The resulting AFB1-N7-dG adduct under...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1609024113

    authors： Lin YC,Owen N,Minko IG,Lange SS,Tomida J,Li L,Stone MP,Wood RD,McCullough AK,Lloyd RS

    更新日期：2016-11-29 00:00:00

  • A family of chromatin remodeling factors related to Williams syndrome transcription factor.

    abstract：:Chromatin remodeling complexes have been implicated in the disruption or reformation of nucleosomal arrays resulting in modulation of transcription, DNA replication, and DNA repair. Here we report the isolation of WCRF, a new chromatin-remodeling complex from HeLa cells. WCRF is composed of two subunits, WCRF135, the ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.97.3.1038

    authors： Bochar DA,Savard J,Wang W,Lafleur DW,Moore P,Côté J,Shiekhattar R

    更新日期：2000-02-01 00:00:00

  • Involvement of {beta}-catenin and unusual behavior of CBP and p300 in glucocorticosteroid signaling in Schwann cells.

    abstract：:In the nervous system, glucocorticosteroid hormones play a major role during development and adult life. Myelin-forming cells are among the targets of glucocorticosteroids, which have been shown to promote myelination both in the central and peripheral nervous system. Glucocorticosteroid-stimulated gene transcription ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0506930102

    authors： Fonte C,Grenier J,Trousson A,Chauchereau A,Lahuna O,Baulieu EE,Schumacher M,Massaad C

    更新日期：2005-10-04 00:00:00

  • Resolution of the novel immune-type receptor gene cluster in zebrafish.

    abstract：:The novel immune-type receptor (NITR) genes encode a unique multigene family of leukocyte regulatory receptors, which possess an extracellular Ig variable (V) domain and may function in innate immunity. Artificial chromosomes that encode zebrafish NITRs have been assembled into a contig spanning approximately 350 kb. ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0405242101

    authors： Yoder JA,Litman RT,Mueller MG,Desai S,Dobrinski KP,Montgomery JS,Buzzeo MP,Ota T,Amemiya CT,Trede NS,Wei S,Djeu JY,Humphray S,Jekosch K,Hernandez Prada JA,Ostrov DA,Litman GW

    更新日期：2004-11-02 00:00:00

  • Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes.

    abstract：:The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.132253599

    authors： Lossos IS,Alizadeh AA,Diehn M,Warnke R,Thorstenson Y,Oefner PJ,Brown PO,Botstein D,Levy R

    更新日期：2002-06-25 00:00:00

  • Evaporation-induced cavitation in nanofluidic channels.

    abstract：:Cavitation, known as the formation of vapor bubbles when liquids are under tension, is of great interest both in condensed matter science as well as in diverse applications such as botany, hydraulic engineering, and medicine. Although widely studied in bulk and microscale-confined liquids, cavitation in the nanoscale ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.1014075109

    authors： Duan C,Karnik R,Lu MC,Majumdar A

    更新日期：2012-03-06 00:00:00

  • Novel free radicals in synthetic and natural pheomelanins: distinction between dopa melanins and cysteinyldopa melanins by ESR spectroscopy.

    abstract：:Synthetic pheomelanins from enzymic oxidation of the 3,4-dihydroxyphenylalanine (dopa) derivative 5-S-cysteinyldopa have been examined by ESR spectroscopy. These alkalisoluble polymers contain a novel kind of free radical that is spectroscopically distinct from that found in eumelanins. Delocalization of the unpaired ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.79.9.2885

    authors： Sealy RC,Hyde JS,Felix CC,Menon IA,Prota G,Swartz HM,Persad S,Haberman HF

    更新日期：1982-05-01 00:00:00

  • Genetic instability in Drosophila melanogaster: De novo induction of putative insertion mutations.

    abstract：:The capacity of a so-called male recombination (MR) chromosome in Drosophila melanogaster to generate mutations at 14 X-chromosome loci specifying visible phenotypes was investigated. Appreciable increases in mutation were found at three loci y, sn, and ras. Tests of represnetative mutants generated at each locus esta...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.74.8.3490

    authors： Green MM

    更新日期：1977-08-01 00:00:00

  • Bursting of sensitive polymersomes induced by curling.

    abstract：:Polymersomes, which are stable and robust vesicles made of block copolymer amphiphiles, are good candidates for drug carriers or micro/nanoreactors. Polymer chemistry enables almost unlimited molecular design of responsive polymersomes whose degradation upon environmental changes has been used for the slow release of ...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.0813157106

    authors： Mabrouk E,Cuvelier D,Brochard-Wyart F,Nassoy P,Li MH

    更新日期：2009-05-05 00:00:00

  • An approach to membrane protein structure without crystals.

    abstract：:The lactose permease of Escherichia coli catalyzes coupled translocation of galactosides and H(+) across the cell membrane. It is the best-characterized member of the Major Facilitator Superfamily, a related group of membrane proteins with 12 transmembrane domains that mediate transport of various substrates across ce...

    journal_title：Proceedings of the National Academy of Sciences of the United States of America

    pub_type： 杂志文章

    doi：10.1073/pnas.182552199

    authors： Sorgen PL,Hu Y,Guan L,Kaback HR,Girvin ME

    更新日期：2002-10-29 00:00:00